Phylogeny and genetic diversity of the Iranian brown bear based on mtDNA control region

The brown bear populations, contrary to other mobile carnivores, exhibit a worldwide genetic structure in several mitochondrial lineages. Populations of the Middle Eastern brown bear, including Iran, are at risk of local extinction. Genetic relationships between the Iranian brown bear and others in the world are still unclear. We sequenced a 614 base pair fragment of the mtDNA control region for 50 brown bears from Iran. The Iranian brown bear presents considerable haplotype diversity (50 individuals, 22 new haplotypes). Mitochondrial sequence analyses revealed one new major mtDNA lineage within Iranian brown bears, comprising 2–3 subclades: (i) Alborz, which includes bears from the Alborz and the Arasbaran Mountains; (ii) Zagros, including individuals from south of East Azerbaijan province to the Southern Zagros Mountains (Kazeroun, Fars province); and (iii) Fars, which comprises bears living in the Southeastern Zagros Mountains (Marvdasht-Eqlid, Fars province). The results of fixation index (FST) and analysis of molecular variance (AMOVA) demonstrate significant genetic structure among the Iranian subclades. Overall, the Iranian brown bears show significant geographic structuring, in addition to the remarkable haplotype diversity.